def test_03_02_00_one(self):
"""Check measurements on a 3x3 square of 1's"""
img = np.array([[0, 0, 0, 0, 0, 0, 0], [0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0], [0, 0, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0]])
ii = II.InjectImage('MyImage', img.astype(float))
ii.module_num = 1
io = II.InjectObjects('MyObjects', img.astype(int))
io.module_num = 2
moi = MOI.MeasureObjectIntensity()
moi.images[0].name.value = 'MyImage'
moi.objects[0].name.value = 'MyObjects'
moi.module_num = 3
pipeline = P.Pipeline()
pipeline.add_listener(self.error_callback)
pipeline.add_module(ii)
pipeline.add_module(io)
pipeline.add_module(moi)
m = pipeline.run()
for category, meas_name, value in (
(MOI.INTENSITY, MOI.INTEGRATED_INTENSITY,
9), (MOI.INTENSITY, MOI.MEAN_INTENSITY,
1), (MOI.INTENSITY, MOI.STD_INTENSITY,
0), (MOI.INTENSITY, MOI.MIN_INTENSITY,
1), (MOI.INTENSITY, MOI.MAX_INTENSITY, 1),
(MOI.INTENSITY, MOI.INTEGRATED_INTENSITY_EDGE,
8), (MOI.INTENSITY, MOI.MEAN_INTENSITY_EDGE,
1), (MOI.INTENSITY, MOI.STD_INTENSITY_EDGE,
0), (MOI.INTENSITY, MOI.MIN_INTENSITY_EDGE,
1), (MOI.INTENSITY, MOI.MAX_INTENSITY_EDGE,
1), (MOI.INTENSITY, MOI.MASS_DISPLACEMENT, 0),
(MOI.INTENSITY, MOI.LOWER_QUARTILE_INTENSITY,
1), (MOI.INTENSITY, MOI.MEDIAN_INTENSITY,
1), (MOI.INTENSITY, MOI.UPPER_QUARTILE_INTENSITY,
1), (MOI.C_LOCATION, MOI.LOC_CMI_X,
3), (MOI.C_LOCATION, MOI.LOC_CMI_Y, 2)):
feature_name = "%s_%s_%s" % (category, meas_name, 'MyImage')
data = m.get_current_measurement('MyObjects', feature_name)
self.assertEqual(np.product(data.shape), 1)
self.assertEqual(
data[0], value,
"%s expected %f != actual %f" % (meas_name, value, data[0]))
def test_03_05_quartiles(self):
"""Regression test a bug that occurs in an image with one pixel"""
labels = np.zeros((10, 20))
labels[2:7, 3:8] = 1
labels[5, 15] = 2
np.random.seed(0)
image = np.random.uniform(size=(10, 20))
ii = II.InjectImage('MyImage', image)
ii.module_num = 1
io = II.InjectObjects('MyObjects', labels)
io.module_num = 2
moi = MOI.MeasureObjectIntensity()
moi.images[0].name.value = 'MyImage'
moi.objects[0].name.value = 'MyObjects'
moi.module_num = 3
pipeline = P.Pipeline()
pipeline.add_listener(self.error_callback)
pipeline.add_module(ii)
pipeline.add_module(io)
pipeline.add_module(moi)
# Crashes when pipeline runs in measureobjectintensity.py revision 7146
m = pipeline.run()
def test_03_01_00_zero(self):
"""Make sure we can process a blank image"""
ii = II.InjectImage('MyImage', np.zeros((10, 10)))
ii.module_num = 1
io = II.InjectObjects('MyObjects', np.zeros((10, 10), int))
io.module_num = 2
moi = MOI.MeasureObjectIntensity()
moi.images[0].name.value = 'MyImage'
moi.objects[0].name.value = 'MyObjects'
moi.module_num = 3
pipeline = P.Pipeline()
pipeline.add_listener(self.error_callback)
pipeline.add_module(ii)
pipeline.add_module(io)
pipeline.add_module(moi)
m = pipeline.run()
for category, features in ((MOI.INTENSITY, MOI.ALL_MEASUREMENTS),
(MOI.C_LOCATION, MOI.ALL_LOCATION_MEASUREMENTS)):
for meas_name in features:
feature_name = "%s_%s_%s" % (category, meas_name, 'MyImage')
data = m.get_current_measurement('MyObjects', feature_name)
self.assertEqual(np.product(data.shape), 0, "Got data for feature %s" % feature_name)
self.features_and_columns_match(m, moi)